Thank you for your reply. I have doubt in output of break dancer thats why i am asking this question. If you see 11 column that include DI_sort.bam|286 and so on... In my output file only DI library is supporting for CTX not the other library DK. So i have doubt that is there any mistake made by me during running breakdancer. It can be possible due to read group problem in libaray.

Both coverage parameter, seq coverage (seqcov) and physical coverage (phycov) is 0 for DK_sort.bam on the other hand sequence coverage is 52 and physical coverage is 175 for DI_sort.bam . So, I suggest you to look into the DK_sort.bam carefully. This might be one of the reason breakdancer is not able to detect supportive read-pair of DK library.